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rename fix STORE/PERATOM to STORE/ATOM

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This commit is contained in:
Axel Kohlmeyer
2023-03-13 22:28:32 -04:00
parent 1031110d93
commit 17f39d9d2c
40 changed files with 199 additions and 145 deletions
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25
doc/src/Developer_notes.rst
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@ -11,6 +11,7 @@ Available topics are:
- `Reading and parsing of text and text files`_
- `Requesting and accessing neighbor lists`_
- `Choosing between a custom atom style, fix property/atom, and fix STORE/ATOM`_
- `Fix contributions to instantaneous energy, virial, and cumulative energy`_
- `KSpace PPPM FFT grids`_
@ -216,6 +217,30 @@ command:
neighbor->add_request(this, "delete_atoms", NeighConst::REQ_FULL);
Choosing between a custom atom style, fix property/atom, and fix STORE/ATOM
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
There are multiple ways to manage per-atom data within LAMMPS. Often
the per-atom storage is only used locally and managed by the class that
uses it. If the data has to persist between multiple time steps and
migrate with atoms when they move from sub-domain to sub-domain or
across periodic boundaries, then using a custom atom style, or :doc:`fix
property/atom <fix_property_atom>`, or the internal fix STORE/ATOM are
possible options.
- Using the atom style is usually the most programming effort and mostly
needed when the per-atom data is an integral part of the model like a
per-atom charge or diameter and thus should be part of the Atoms
section of a :doc:`data file <read_data>`.
- Fix property/atom is useful if the data is optional or should be
entered by the user, or accessed as a (named) custom property. In this
case the fix should be entered as part of the input (and not
internally) which allows to enter and store its content with data files.
- Fix STORE/ATOM should be used when the data should be accessed internally
only and thus the fix can be created internally.
Fix contributions to instantaneous energy, virial, and cumulative energy
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

29
doc/src/Developer_updating.rst
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@ -24,6 +24,7 @@ Available topics in mostly chronological order are:
- `Use of "override" instead of "virtual"`_
- `Simplified and more compact neighbor list requests`_
- `Split of fix STORE into fix STORE/GLOBAL and fix STORE/PERATOM`_
- `Rename of fix STORE/PERATOM to fix STORE/ATOM and change of arguments`_
- `Use Output::get_dump_by_id() instead of Output::find_dump()`_
- `Refactored grid communication using Grid3d/Grid2d classes instead of GridComm`_
@ -385,6 +386,34 @@ New:
This change is **required** or else the code will not compile.
Rename of fix STORE/PERATOM to fix STORE/ATOM and change of arguments
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: TBD
The available functionality of the internal fix to store per-atom
properties was expanded to enable storing data with ghost atoms and to
support binary restart files. With those changes, the fix was renamed
to fix STORE/ATOM and the number and order of (required) arguments has
changed.
Old syntax: ``ID group-ID STORE/PERATOM rflag n1 n2 [n3]``
- *rflag* = 0/1, *no*/*yes* store per-atom values in restart file
- :math:`n1 = 1, n2 = 1, \mathrm{no}\;n3 \to` per-atom vector, single value per atom
- :math:`n1 = 1, n2 > 1, \mathrm{no}\;n3 \to` per-atom array, *n2* values per atom
- :math:`n1 = 1, n2 > 0, n3 > 0 \to` per-atom tensor, *n2* x *n3* values per atom
New syntax: ``ID group-ID STORE/ATOM n1 n2 gflag rflag``
- :math:`n1 = 1, n2 = 0 \to` per-atom vector, single value per atom
- :math:`n1 > 1, n2 = 0 \to` per-atom array, *n1* values per atom
- :math:`n1 > 0, n2 > 0 \to` per-atom tensor, *n1* x *n2* values per atom
- *gflag* = 0/1, *no*/*yes* communicate per-atom values with ghost atoms
- *rflag* = 0/1, *no*/*yes* store per-atom values in restart file
Since this is an internal fix, there is no user visible change.
Use Output::get_dump_by_id() instead of Output::find_dump()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

2
src/AMOEBA/amoeba_induce.cpp
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@ -19,7 +19,7 @@
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "fix_store_peratom.h"
#include "fix_store_atom.h"
#include "math_const.h"
#include "math_special.h"
#include "my_page.h"

2
src/AMOEBA/amoeba_utils.cpp
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@ -17,7 +17,7 @@
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "fix_store_peratom.h"
#include "fix_store_atom.h"
#include "neigh_list.h"
#include <cmath>

26
src/AMOEBA/pair_amoeba.cpp
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@ -20,7 +20,7 @@
#include "domain.h"
#include "error.h"
#include "fix.h"
#include "fix_store_peratom.h"
#include "fix_store_atom.h"
#include "force.h"
#include "group.h"
#include "math_special.h"
@ -861,8 +861,8 @@ void PairAmoeba::init_style()
Fix *myfix;
if (first_flag) {
id_pole = utils::strdup("AMOEBA_pole");
myfix = modify->add_fix(fmt::format("{} {} STORE/PERATOM 13 0 0 1",id_pole,group->names[0]));
fixpole = dynamic_cast<FixStorePeratom *>(myfix);
myfix = modify->add_fix(fmt::format("{} {} STORE/ATOM 13 0 0 1",id_pole,group->names[0]));
fixpole = dynamic_cast<FixStoreAtom *>(myfix);
}
// creation of per-atom storage
@ -873,14 +873,14 @@ void PairAmoeba::init_style()
if (first_flag && use_pred) {
id_udalt = utils::strdup("AMOEBA_udalt");
myfix = modify->add_fix(fmt::format("{} {} STORE/PERATOM {} 3 0 1",
myfix = modify->add_fix(fmt::format("{} {} STORE/ATOM {} 3 0 1",
id_udalt, group->names[0], maxualt));
fixudalt = dynamic_cast<FixStorePeratom *>(myfix);
fixudalt = dynamic_cast<FixStoreAtom *>(myfix);
id_upalt = utils::strdup("AMOEBA_upalt");
myfix = modify->add_fix(fmt::format("{} {} STORE/PERATOM {} 3 0 1",
myfix = modify->add_fix(fmt::format("{} {} STORE/ATOM {} 3 0 1",
id_upalt, group->names[0], maxualt));
fixupalt = dynamic_cast<FixStorePeratom *>(myfix);
fixupalt = dynamic_cast<FixStoreAtom *>(myfix);
}
// create pages for storing pairwise data:
@ -995,21 +995,21 @@ void PairAmoeba::init_style()
if (id_pole) {
myfix = modify->get_fix_by_id(id_pole);
if (!myfix)
error->all(FLERR,"Could not find internal pair amoeba fix STORE/PERATOM id {}", id_pole);
fixpole = dynamic_cast<FixStorePeratom *>(myfix);
error->all(FLERR,"Could not find internal pair amoeba fix STORE/ATOM id {}", id_pole);
fixpole = dynamic_cast<FixStoreAtom *>(myfix);
}
if (id_udalt) {
myfix = modify->get_fix_by_id(id_udalt);
if (!myfix)
error->all(FLERR,"Could not find internal pair amoeba fix STORE/PERATOM id {}", id_udalt);
fixudalt = dynamic_cast<FixStorePeratom *>(myfix);
error->all(FLERR,"Could not find internal pair amoeba fix STORE/ATOM id {}", id_udalt);
fixudalt = dynamic_cast<FixStoreAtom *>(myfix);
myfix = modify->get_fix_by_id(id_upalt);
if (!myfix)
error->all(FLERR,"Could not find internal pair amoeba fix STORE/PERATOM id {}", id_upalt);
fixupalt = dynamic_cast<FixStorePeratom *>(myfix);
error->all(FLERR,"Could not find internal pair amoeba fix STORE/ATOM id {}", id_upalt);
fixupalt = dynamic_cast<FixStoreAtom *>(myfix);
}
// assign hydrogen neighbors (redID) to each owned atom

6
src/AMOEBA/pair_amoeba.h
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@ -166,9 +166,9 @@ class PairAmoeba : public Pair {
int *amgroup; // AMOEBA polarization group, 1 to Ngroup
char *id_pole, *id_udalt, *id_upalt;
class FixStorePeratom *fixpole; // stores pole = multipole components
class FixStorePeratom *fixudalt; // stores udalt = induced dipole history
class FixStorePeratom *fixupalt; // stores upalt = induced dipole history
class FixStoreAtom *fixpole; // stores pole = multipole components
class FixStoreAtom *fixudalt; // stores udalt = induced dipole history
class FixStoreAtom *fixupalt; // stores upalt = induced dipole history
// static per-type properties defined in force-field file

6
src/CORESHELL/compute_temp_cs.cpp
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@ -24,7 +24,7 @@
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "fix_store_peratom.h"
#include "fix_store_atom.h"
#include "force.h"
#include "group.h"
#include "memory.h"
@ -67,8 +67,8 @@ ComputeTempCS::ComputeTempCS(LAMMPS *lmp, int narg, char **arg) :
// id = compute-ID + COMPUTE_STORE, fix group = compute group
id_fix = utils::strdup(id + std::string("_COMPUTE_STORE"));
fix = dynamic_cast<FixStorePeratom *>(
modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 0 0 0", id_fix, group->names[igroup])));
fix = dynamic_cast<FixStoreAtom *>(
modify->add_fix(fmt::format("{} {} STORE/ATOM 1 0 0 0", id_fix, group->names[igroup])));
// set fix store values = 0 for now
// fill them in via setup() once Comm::borders() has been called

2
src/CORESHELL/compute_temp_cs.h
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@ -54,7 +54,7 @@ class ComputeTempCS : public Compute {
double **vint;
char *id_fix;
class FixStorePeratom *fix;
class FixStoreAtom *fix;
void dof_compute();
void vcm_pairs();

8
src/EXTRA-COMPUTE/compute_hma.cpp
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@ -54,7 +54,7 @@ https://doi.org/10.1103/PhysRevE.92.043303
#include "domain.h"
#include "error.h"
#include "fix.h"
#include "fix_store_peratom.h"
#include "fix_store_atom.h"
#include "force.h"
#include "group.h"
#include "improper.h"
@ -90,8 +90,8 @@ ComputeHMA::ComputeHMA(LAMMPS *lmp, int narg, char **arg) :
// our new fix's group = same as compute group
id_fix = utils::strdup(std::string(id)+"_COMPUTE_STORE");
fix = dynamic_cast<FixStorePeratom *>(
modify->add_fix(fmt::format("{} {} STORE/PERATOM 3 0 0 1", id_fix, group->names[igroup])));
fix = dynamic_cast<FixStoreAtom *>(
modify->add_fix(fmt::format("{} {} STORE/ATOM 3 0 0 1", id_fix, group->names[igroup])));
// calculate xu,yu,zu for fix store array
// skip if reset from restart file
@ -196,7 +196,7 @@ void ComputeHMA::setup()
// set fix which stores original atom coords
fix = dynamic_cast<FixStorePeratom *>(modify->get_fix_by_id(id_fix));
fix = dynamic_cast<FixStoreAtom *>(modify->get_fix_by_id(id_fix));
if (!fix) error->all(FLERR,"Could not find hma per-atom store fix ID {}", id_fix);
}

2
src/EXTRA-COMPUTE/compute_hma.h
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@ -43,7 +43,7 @@ class ComputeHMA : public Compute {
char *id_fix;
char *id_temp;
double finaltemp;
class FixStorePeratom *fix;
class FixStoreAtom *fix;
double boltz, nktv2p, inv_volume;
double deltaPcap;
double virial_compute(int);

2
src/EXTRA-COMPUTE/compute_msd_nongauss.cpp
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@ -19,7 +19,7 @@
#include "atom.h"
#include "domain.h"
#include "fix_store_peratom.h"
#include "fix_store_atom.h"
#include "group.h"
#include "update.h"

10
src/EXTRA-MOLECULE/bond_harmonic_restrain.cpp
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@ -17,7 +17,7 @@
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "fix_store_peratom.h"
#include "fix_store_atom.h"
#include "force.h"
#include "memory.h"
#include "modify.h"
@ -162,8 +162,8 @@ void BondHarmonicRestrain::init_style()
if (natoms < 0) {
// create internal fix to store initial positions
initial = dynamic_cast<FixStorePeratom *>(
modify->add_fix("BOND_RESTRAIN_X0 all STORE/PERATOM 3 0 1 1"));
initial = dynamic_cast<FixStoreAtom *>(
modify->add_fix("BOND_RESTRAIN_X0 all STORE/ATOM 3 0 1 1"));
if (!initial) error->all(FLERR, "Failure to create internal per-atom storage");
natoms = atom->natoms;
@ -178,8 +178,8 @@ void BondHarmonicRestrain::init_style()
// we add the fix, but do not initialize it. It will pull the data from the restart.
if (!initial) {
initial = dynamic_cast<FixStorePeratom *>(
modify->add_fix("BOND_RESTRAIN_X0 all STORE/PERATOM 3 0 1 1"));
initial = dynamic_cast<FixStoreAtom *>(
modify->add_fix("BOND_RESTRAIN_X0 all STORE/ATOM 3 0 1 1"));
if (!initial) error->all(FLERR, "Failure to create internal per-atom storage");
}
}

2
src/EXTRA-MOLECULE/bond_harmonic_restrain.h
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@ -41,7 +41,7 @@ class BondHarmonicRestrain : public Bond {
protected:
double *k;
bigint natoms;
class FixStorePeratom *initial;
class FixStoreAtom *initial;
virtual void allocate();
};

14
src/FEP/fix_adapt_fep.cpp
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@ -20,7 +20,7 @@
#include "atom.h"
#include "error.h"
#include "fix_store_peratom.h"
#include "fix_store_atom.h"
#include "force.h"
#include "group.h"
#include "input.h"
@ -211,8 +211,8 @@ void FixAdaptFEP::post_constructor()
if (diamflag) {
id_fix_diam = utils::strdup(id + std::string("_FIX_STORE_DIAM"));
fix_diam = dynamic_cast<FixStorePeratom *>(
modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 0 0 1", id_fix_diam,group->names[igroup])));
fix_diam = dynamic_cast<FixStoreAtom *>(
modify->add_fix(fmt::format("{} {} STORE/ATOM 1 0 0 1", id_fix_diam,group->names[igroup])));
if (fix_diam->restart_reset) fix_diam->restart_reset = 0;
else {
double *vec = fix_diam->vstore;
@ -229,8 +229,8 @@ void FixAdaptFEP::post_constructor()
if (chgflag) {
id_fix_chg = utils::strdup(id + std::string("_FIX_STORE_CHG"));
fix_chg = dynamic_cast<FixStorePeratom *>(
modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 0 0 1",id_fix_chg,group->names[igroup])));
fix_chg = dynamic_cast<FixStoreAtom *>(
modify->add_fix(fmt::format("{} {} STORE/ATOM 1 0 0 1",id_fix_chg,group->names[igroup])));
if (fix_chg->restart_reset) fix_chg->restart_reset = 0;
else {
double *vec = fix_chg->vstore;
@ -333,11 +333,11 @@ void FixAdaptFEP::init()
// fixes that store initial per-atom values
if (id_fix_diam) {
fix_diam = dynamic_cast<FixStorePeratom *>(modify->get_fix_by_id(id_fix_diam));
fix_diam = dynamic_cast<FixStoreAtom *>(modify->get_fix_by_id(id_fix_diam));
if (!fix_diam) error->all(FLERR,"Could not find fix adapt/fep storage fix ID {}", id_fix_diam);
}
if (id_fix_chg) {
fix_chg = dynamic_cast<FixStorePeratom *>(modify->get_fix_by_id(id_fix_chg));
fix_chg = dynamic_cast<FixStoreAtom *>(modify->get_fix_by_id(id_fix_chg));
if (!fix_chg) error->all(FLERR,"Could not find fix adapt/fep storage fix ID {}", id_fix_chg);
}

2
src/FEP/fix_adapt_fep.h
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@ -46,7 +46,7 @@ class FixAdaptFEP : public Fix {
int anypair;
int nlevels_respa;
char *id_fix_diam, *id_fix_chg;
class FixStorePeratom *fix_diam, *fix_chg;
class FixStoreAtom *fix_diam, *fix_chg;
struct Adapt {
int which, ivar;

2
src/GPU/pair_amoeba_gpu.cpp
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@ -23,7 +23,7 @@
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "fix_store_peratom.h"
#include "fix_store_atom.h"
#include "force.h"
#include "gpu_extra.h"
#include "info.h"

2
src/GPU/pair_hippo_gpu.cpp
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@ -23,7 +23,7 @@
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "fix_store_peratom.h"
#include "fix_store_atom.h"
#include "force.h"
#include "gpu_extra.h"
#include "info.h"

6
src/REPLICA/tad.cpp
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@ -24,7 +24,7 @@
#include "error.h"
#include "finish.h"
#include "fix_event_tad.h"
#include "fix_store_peratom.h"
#include "fix_store_atom.h"
#include "force.h"
#include "integrate.h"
#include "memory.h"
@ -133,9 +133,9 @@ void TAD::command(int narg, char **arg)
fix_event = dynamic_cast<FixEventTAD *>(modify->add_fix("tad_event all EVENT/TAD"));
// create FixStorePeratom object to store revert state
// create FixStoreAtom object to store revert state
fix_revert = dynamic_cast<FixStorePeratom *>(modify->add_fix("tad_revert all STORE/PERATOM 7 0 0 0"));
fix_revert = dynamic_cast<FixStoreAtom *>(modify->add_fix("tad_revert all STORE/ATOM 7 0 0 0"));
// create Finish for timing output

18
src/REPLICA/tad.h
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@ -48,15 +48,15 @@ class TAD : public Command {
double time_dynamics, time_quench, time_neb, time_comm, time_output;
double time_start;
class NEB *neb; // NEB object
class Fix *fix_neb; // FixNEB object
class Compute *compute_event; // compute to detect event
class FixEventTAD *fix_event; // current event/state
class FixStorePeratom *fix_revert; // revert state
FixEventTAD **fix_event_list; // list of possible events
int n_event_list; // number of events
int nmax_event_list; // allocated events
int nmin_event_list; // minimum allocation
class NEB *neb; // NEB object
class Fix *fix_neb; // FixNEB object
class Compute *compute_event; // compute to detect event
class FixEventTAD *fix_event; // current event/state
class FixStoreAtom *fix_revert; // revert state
FixEventTAD **fix_event_list; // list of possible events
int n_event_list; // number of events
int nmax_event_list; // allocated events
int nmin_event_list; // minimum allocation
char *neb_logfilename; // filename for ulogfile_neb
FILE *uscreen_neb; // neb universe screen output

10
src/VTK/dump_vtk.cpp
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@ -31,7 +31,7 @@
#include "domain.h"
#include "error.h"
#include "fix.h"
#include "fix_store_peratom.h"
#include "fix_store_atom.h"
#include "force.h"
#include "group.h"
#include "input.h"
@ -2357,16 +2357,16 @@ int DumpVTK::modify_param(int narg, char **arg)
thresh_value[nthresh] = utils::numeric(FLERR,arg[3],false,lmp);
thresh_last[nthresh] = -1;
} else {
thresh_fix = (FixStorePeratom **)
memory->srealloc(thresh_fix,(nthreshlast+1)*sizeof(FixStorePeratom *),"dump:thresh_fix");
thresh_fix = (FixStoreAtom **)
memory->srealloc(thresh_fix,(nthreshlast+1)*sizeof(FixStoreAtom *),"dump:thresh_fix");
thresh_fixID = (char **)
memory->srealloc(thresh_fixID,(nthreshlast+1)*sizeof(char *),"dump:thresh_fixID");
memory->grow(thresh_first,(nthreshlast+1),"dump:thresh_first");
std::string threshid = fmt::format("{}{}_DUMP_STORE",id,nthreshlast);
thresh_fixID[nthreshlast] = utils::strdup(threshid);
threshid += fmt::format(" {} STORE/PERATOM 1 0 0 1", group->names[igroup]);
thresh_fix[nthreshlast] = dynamic_cast<FixStorePeratom *>(modify->add_fix(threshid));
threshid += fmt::format(" {} STORE/ATOM 1 0 0 1", group->names[igroup]);
thresh_fix[nthreshlast] = dynamic_cast<FixStoreAtom *>(modify->add_fix(threshid));
thresh_last[nthreshlast] = nthreshlast;
thresh_first[nthreshlast] = 1;

6
src/balance.cpp
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@ -26,7 +26,7 @@
#include "neighbor.h"
#include "comm.h"
#include "domain.h"
#include "fix_store_peratom.h"
#include "fix_store_atom.h"
#include "force.h"
#include "imbalance.h"
#include "imbalance_group.h"
@ -513,9 +513,9 @@ void Balance::weight_storage(char *prefix)
if (prefix) cmd = prefix;
cmd += "IMBALANCE_WEIGHTS";
fixstore = dynamic_cast<FixStorePeratom *>(modify->get_fix_by_id(cmd));
fixstore = dynamic_cast<FixStoreAtom *>(modify->get_fix_by_id(cmd));
if (!fixstore)
fixstore = dynamic_cast<FixStorePeratom *>(modify->add_fix(cmd + " all STORE/PERATOM 1 0 0 0"));
fixstore = dynamic_cast<FixStoreAtom *>(modify->add_fix(cmd + " all STORE/ATOM 1 0 0 0"));
// do not carry weights with atoms during normal atom migration

10
src/balance.h
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@ -27,11 +27,11 @@ namespace LAMMPS_NS {
class Balance : public Command {
public:
class RCB *rcb;
class FixStorePeratom *fixstore; // per-atom weights stored in FixStorePeratom
int wtflag; // 1 if particle weighting is used
int varflag; // 1 if weight style var(iable) is used
int sortflag; // 1 if sorting of comm messages is done
int outflag; // 1 for output of balance results to file
class FixStoreAtom *fixstore; // per-atom weights stored in FixStorePeratom
int wtflag; // 1 if particle weighting is used
int varflag; // 1 if weight style var(iable) is used
int sortflag; // 1 if sorting of comm messages is done
int outflag; // 1 for output of balance results to file
Balance(class LAMMPS *);
~Balance() override;

6
src/compute_chunk_atom.cpp
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@ -21,7 +21,7 @@
#include "domain.h"
#include "error.h"
#include "fix.h"
#include "fix_store_peratom.h"
#include "fix_store_atom.h"
#include "group.h"
#include "input.h"
#include "lattice.h"
@ -571,8 +571,8 @@ void ComputeChunkAtom::init()
if ((idsflag == ONCE || lockcount) && !fixstore) {
id_fix = utils::strdup(id + std::string("_COMPUTE_STORE"));
fixstore = dynamic_cast<FixStorePeratom *>(
modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 0 0 1", id_fix, group->names[igroup])));
fixstore = dynamic_cast<FixStoreAtom *>(
modify->add_fix(fmt::format("{} {} STORE/ATOM 1 0 0 1", id_fix, group->names[igroup])));
}
if ((idsflag != ONCE && !lockcount) && fixstore) {

2
src/compute_chunk_atom.h
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@ -93,7 +93,7 @@ class ComputeChunkAtom : public Compute {
double *varatom;
char *id_fix;
class FixStorePeratom *fixstore;
class FixStoreAtom *fixstore;
class Fix *lockfix; // ptr to FixAveChunk that is locking out setups
// null pointer if no lock currently in place

8
src/compute_displace_atom.cpp
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@ -17,7 +17,7 @@
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "fix_store_peratom.h"
#include "fix_store_atom.h"
#include "group.h"
#include "input.h"
#include "memory.h"
@ -74,8 +74,8 @@ ComputeDisplaceAtom::ComputeDisplaceAtom(LAMMPS *lmp, int narg, char **arg) :
// id = compute-ID + COMPUTE_STORE, fix group = compute group
id_fix = utils::strdup(std::string(id) + "_COMPUTE_STORE");
fix = dynamic_cast<FixStorePeratom *>(
modify->add_fix(fmt::format("{} {} STORE/PERATOM 3 0 0 1", id_fix, group->names[igroup])));
fix = dynamic_cast<FixStoreAtom *>(
modify->add_fix(fmt::format("{} {} STORE/ATOM 3 0 0 1", id_fix, group->names[igroup])));
// calculate xu,yu,zu for fix store array
// skip if reset from restart file
@ -120,7 +120,7 @@ void ComputeDisplaceAtom::init()
{
// set fix which stores original atom coords
fix = dynamic_cast<FixStorePeratom *>(modify->get_fix_by_id(id_fix));
fix = dynamic_cast<FixStoreAtom *>(modify->get_fix_by_id(id_fix));
if (!fix) error->all(FLERR,"Could not find compute displace/atom fix with ID {}", id_fix);
if (refreshflag) {

2
src/compute_displace_atom.h
View File

@ -38,7 +38,7 @@ class ComputeDisplaceAtom : public Compute {
int nmax;
double **displace;
char *id_fix;
class FixStorePeratom *fix;
class FixStoreAtom *fix;
int refreshflag, ivar, nvmax; // refresh option is enabled
char *rvar; // for incremental dumps

8
src/compute_msd.cpp
View File

@ -16,7 +16,7 @@
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "fix_store_peratom.h"
#include "fix_store_atom.h"
#include "group.h"
#include "modify.h"
#include "update.h"
@ -63,8 +63,8 @@ ComputeMSD::ComputeMSD(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, a
// id = compute-ID + COMPUTE_STORE, fix group = compute group
id_fix = utils::strdup(id + std::string("_COMPUTE_STORE"));
fix = dynamic_cast<FixStorePeratom *>(
modify->add_fix(fmt::format("{} {} STORE/PERATOM 3 0 0 1", id_fix, group->names[igroup])));
fix = dynamic_cast<FixStoreAtom *>(
modify->add_fix(fmt::format("{} {} STORE/ATOM 3 0 0 1", id_fix, group->names[igroup])));
// calculate xu,yu,zu for fix store array
// skip if reset from restart file
@ -127,7 +127,7 @@ void ComputeMSD::init()
{
// set fix which stores reference atom coords
fix = dynamic_cast<FixStorePeratom *>(modify->get_fix_by_id(id_fix));
fix = dynamic_cast<FixStoreAtom *>(modify->get_fix_by_id(id_fix));
if (!fix) error->all(FLERR, "Could not find compute msd fix with ID {}", id_fix);
// nmsd = # of atoms in group

2
src/compute_msd.h
View File

@ -39,7 +39,7 @@ class ComputeMSD : public Compute {
bigint nmsd;
double masstotal;
char *id_fix;
class FixStorePeratom *fix;
class FixStoreAtom *fix;
};
} // namespace LAMMPS_NS

8
src/compute_vacf.cpp
View File

@ -18,7 +18,7 @@
#include "update.h"
#include "group.h"
#include "modify.h"
#include "fix_store_peratom.h"
#include "fix_store_atom.h"
#include "error.h"
using namespace LAMMPS_NS;
@ -39,8 +39,8 @@ ComputeVACF::ComputeVACF(LAMMPS *lmp, int narg, char **arg) :
// id = compute-ID + COMPUTE_STORE, fix group = compute group
id_fix = utils::strdup(id + std::string("_COMPUTE_STORE"));
fix = dynamic_cast<FixStorePeratom *>(
modify->add_fix(fmt::format("{} {} STORE/PERATOM 3 0 0 1", id_fix, group->names[igroup])));
fix = dynamic_cast<FixStoreAtom *>(
modify->add_fix(fmt::format("{} {} STORE/ATOM 3 0 0 1", id_fix, group->names[igroup])));
// store current velocities in fix store array
// skip if reset from restart file
@ -84,7 +84,7 @@ void ComputeVACF::init()
{
// set fix which stores original atom velocities
fix = dynamic_cast<FixStorePeratom *>(modify->get_fix_by_id(id_fix));
fix = dynamic_cast<FixStoreAtom *>(modify->get_fix_by_id(id_fix));
if (!fix) error->all(FLERR,"Could not find compute vacf fix ID {}", id_fix);
// nvacf = # of atoms in group

2
src/compute_vacf.h
View File

@ -35,7 +35,7 @@ class ComputeVACF : public Compute {
protected:
bigint nvacf;
char *id_fix;
class FixStorePeratom *fix;
class FixStoreAtom *fix;
};
} // namespace LAMMPS_NS

10
src/dump_custom.cpp
View File

@ -20,7 +20,7 @@
#include "domain.h"
#include "error.h"
#include "fix.h"
#include "fix_store_peratom.h"
#include "fix_store_atom.h"
#include "group.h"
#include "input.h"
#include "memory.h"
@ -2005,16 +2005,16 @@ int DumpCustom::modify_param(int narg, char **arg)
thresh_value[nthresh] = utils::numeric(FLERR,arg[3],false,lmp);
thresh_last[nthresh] = -1;
} else {
thresh_fix = (FixStorePeratom **)
memory->srealloc(thresh_fix,(nthreshlast+1)*sizeof(FixStorePeratom *),"dump:thresh_fix");
thresh_fix = (FixStoreAtom **)
memory->srealloc(thresh_fix,(nthreshlast+1)*sizeof(FixStoreAtom *),"dump:thresh_fix");
thresh_fixID = (char **)
memory->srealloc(thresh_fixID,(nthreshlast+1)*sizeof(char *),"dump:thresh_fixID");
memory->grow(thresh_first,(nthreshlast+1),"dump:thresh_first");
std::string threshid = fmt::format("{}{}_DUMP_STORE",id,nthreshlast);
thresh_fixID[nthreshlast] = utils::strdup(threshid);
threshid += fmt::format(" {} STORE/PERATOM 1 0 0 1", group->names[igroup]);
thresh_fix[nthreshlast] = dynamic_cast<FixStorePeratom *>(modify->add_fix(threshid));
threshid += fmt::format(" {} STORE/ATOM 1 0 0 1", group->names[igroup]);
thresh_fix[nthreshlast] = dynamic_cast<FixStoreAtom *>(modify->add_fix(threshid));
thresh_last[nthreshlast] = nthreshlast;
thresh_first[nthreshlast] = 1;

26
src/dump_custom.h
View File

@ -37,19 +37,19 @@ class DumpCustom : public Dump {
int nevery; // dump frequency for output
char *idregion; // region ID, nullptr if no region
int nthresh; // # of defined thresholds
int nthreshlast; // # of defined thresholds with value = LAST
//
int *thresh_array; // array to threshold on for each nthresh
int *thresh_op; // threshold operation for each nthresh
double *thresh_value; // threshold value for each nthresh
int *thresh_last; // for threshold value = LAST,
// index into thresh_fix
// -1 if not LAST, value is numeric
//
class FixStorePeratom **thresh_fix; // stores values for each threshold LAST
char **thresh_fixID; // IDs of thresh_fixes
int *thresh_first; // 1 the first time a FixStore values accessed
int nthresh; // # of defined thresholds
int nthreshlast; // # of defined thresholds with value = LAST
//
int *thresh_array; // array to threshold on for each nthresh
int *thresh_op; // threshold operation for each nthresh
double *thresh_value; // threshold value for each nthresh
int *thresh_last; // for threshold value = LAST,
// index into thresh_fix
// -1 if not LAST, value is numeric
//
class FixStoreAtom **thresh_fix; // stores values for each threshold LAST
char **thresh_fixID; // IDs of thresh_fixes
int *thresh_first; // 1 the first time a FixStore values accessed
int expand; // flag for whether field args were expanded
char **earg; // field names with wildcard expansion

14
src/fix_adapt.cpp
View File

@ -19,7 +19,7 @@
#include "bond.h"
#include "domain.h"
#include "error.h"
#include "fix_store_peratom.h"
#include "fix_store_atom.h"
#include "force.h"
#include "group.h"
#include "input.h"
@ -278,8 +278,8 @@ void FixAdapt::post_constructor()
if (diamflag && atom->radius_flag) {
id_fix_diam = utils::strdup(id + std::string("_FIX_STORE_DIAM"));
fix_diam = dynamic_cast<FixStorePeratom *>(
modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 0 0 1", id_fix_diam,group->names[igroup])));
fix_diam = dynamic_cast<FixStoreAtom *>(
modify->add_fix(fmt::format("{} {} STORE/ATOM 1 0 0 1", id_fix_diam,group->names[igroup])));
if (fix_diam->restart_reset) fix_diam->restart_reset = 0;
else {
double *vec = fix_diam->vstore;
@ -296,8 +296,8 @@ void FixAdapt::post_constructor()
if (chgflag && atom->q_flag) {
id_fix_chg = utils::strdup(id + std::string("_FIX_STORE_CHG"));
fix_chg = dynamic_cast<FixStorePeratom *>(
modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 0 0 1",id_fix_chg,group->names[igroup])));
fix_chg = dynamic_cast<FixStoreAtom *>(
modify->add_fix(fmt::format("{} {} STORE/ATOM 1 0 0 1",id_fix_chg,group->names[igroup])));
if (fix_chg->restart_reset) fix_chg->restart_reset = 0;
else {
double *vec = fix_chg->vstore;
@ -494,11 +494,11 @@ void FixAdapt::init()
// fixes that store initial per-atom values
if (id_fix_diam) {
fix_diam = dynamic_cast<FixStorePeratom *>(modify->get_fix_by_id(id_fix_diam));
fix_diam = dynamic_cast<FixStoreAtom *>(modify->get_fix_by_id(id_fix_diam));
if (!fix_diam) error->all(FLERR,"Could not find fix adapt storage fix ID {}", id_fix_diam);
}
if (id_fix_chg) {
fix_chg = dynamic_cast<FixStorePeratom *>(modify->get_fix_by_id(id_fix_chg));
fix_chg = dynamic_cast<FixStoreAtom *>(modify->get_fix_by_id(id_fix_chg));
if (!fix_chg) error->all(FLERR,"Could not find fix adapt storage fix ID {}", id_fix_chg);
}

2
src/fix_adapt.h
View File

@ -48,7 +48,7 @@ class FixAdapt : public Fix {
int anypair, anybond, anyangle;
int nlevels_respa;
char *id_fix_diam, *id_fix_chg;
class FixStorePeratom *fix_diam, *fix_chg;
class FixStoreAtom *fix_diam, *fix_chg;
double previous_diam_scale, previous_chg_scale;
int discflag;

2
src/fix_balance.cpp
View File

@ -19,7 +19,7 @@
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "fix_store_peratom.h"
#include "fix_store_atom.h"
#include "force.h"
#include "irregular.h"
#include "kspace.h"

38
src/fix_store_peratom.cpp → src/fix_store_atom.cpp
View File

@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "fix_store_peratom.h"
#include "fix_store_atom.h"
#include "atom.h"
#include "error.h"
@ -32,10 +32,10 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixStorePeratom::FixStorePeratom(LAMMPS *lmp, int narg, char **arg) :
FixStoreAtom::FixStoreAtom(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), vstore(nullptr), astore(nullptr)
{
if (narg != 7) error->all(FLERR, "Illegal fix STORE/PERATOM command: number of args");
if (narg != 7) error->all(FLERR, "Illegal fix STORE/ATOM command: number of args");
disable = 0;
@ -52,7 +52,7 @@ FixStorePeratom::FixStorePeratom(LAMMPS *lmp, int narg, char **arg) :
else if (n1 > 0 && n2 > 0)
tensorflag = 1;
else
error->all(FLERR, "Illegal fix STORE/PERATOM dimension args: {} {}", n1, n2);
error->all(FLERR, "Illegal fix STORE/ATOM dimension args: {} {}", n1, n2);
if (vecflag || arrayflag)
nvalues = n1;
@ -71,7 +71,7 @@ FixStorePeratom::FixStorePeratom(LAMMPS *lmp, int narg, char **arg) :
astore = nullptr;
tstore = nullptr;
FixStorePeratom::grow_arrays(atom->nmax);
FixStoreAtom::grow_arrays(atom->nmax);
atom->add_callback(Atom::GROW);
if (restartflag) atom->add_callback(Atom::RESTART);
if (ghostflag) atom->add_callback(Atom::BORDER);
@ -93,7 +93,7 @@ FixStorePeratom::FixStorePeratom(LAMMPS *lmp, int narg, char **arg) :
/* ---------------------------------------------------------------------- */
FixStorePeratom::~FixStorePeratom()
FixStoreAtom::~FixStoreAtom()
{
// unregister callbacks to this fix from Atom class
@ -108,7 +108,7 @@ FixStorePeratom::~FixStorePeratom()
/* ---------------------------------------------------------------------- */
int FixStorePeratom::setmask()
int FixStoreAtom::setmask()
{
int mask = 0;
return mask;
@ -118,7 +118,7 @@ int FixStorePeratom::setmask()
allocate atom-based array
------------------------------------------------------------------------- */
void FixStorePeratom::grow_arrays(int nmax)
void FixStoreAtom::grow_arrays(int nmax)
{
if (vecflag)
memory->grow(vstore, nmax, "store:vstore");
@ -132,7 +132,7 @@ void FixStorePeratom::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
void FixStorePeratom::copy_arrays(int i, int j, int /*delflag*/)
void FixStoreAtom::copy_arrays(int i, int j, int /*delflag*/)
{
if (disable) return;
@ -149,7 +149,7 @@ void FixStorePeratom::copy_arrays(int i, int j, int /*delflag*/)
pack values for border communication at re-neighboring
------------------------------------------------------------------------- */
int FixStorePeratom::pack_border(int n, int *list, double *buf)
int FixStoreAtom::pack_border(int n, int *list, double *buf)
{
int i, j, k;
@ -179,7 +179,7 @@ int FixStorePeratom::pack_border(int n, int *list, double *buf)
unpack values for border communication at re-neighboring
------------------------------------------------------------------------- */
int FixStorePeratom::unpack_border(int n, int first, double *buf)
int FixStoreAtom::unpack_border(int n, int first, double *buf)
{
int i, k, last;
@ -203,7 +203,7 @@ int FixStorePeratom::unpack_border(int n, int first, double *buf)
pack values in local atom-based array for exchange with another proc
------------------------------------------------------------------------- */
int FixStorePeratom::pack_exchange(int i, double *buf)
int FixStoreAtom::pack_exchange(int i, double *buf)
{
if (disable) return 0;
@ -222,7 +222,7 @@ int FixStorePeratom::pack_exchange(int i, double *buf)
unpack values in local atom-based array from exchange with another proc
------------------------------------------------------------------------- */
int FixStorePeratom::unpack_exchange(int nlocal, double *buf)
int FixStoreAtom::unpack_exchange(int nlocal, double *buf)
{
if (disable) return 0;
@ -241,7 +241,7 @@ int FixStorePeratom::unpack_exchange(int nlocal, double *buf)
pack values in local atom-based arrays for restart file
------------------------------------------------------------------------- */
int FixStorePeratom::pack_restart(int i, double *buf)
int FixStoreAtom::pack_restart(int i, double *buf)
{
if (disable) {
buf[0] = 0;
@ -266,7 +266,7 @@ int FixStorePeratom::pack_restart(int i, double *buf)
unpack values from atom->extra array to restart the fix
------------------------------------------------------------------------- */
void FixStorePeratom::unpack_restart(int nlocal, int nth)
void FixStoreAtom::unpack_restart(int nlocal, int nth)
{
if (disable) return;
@ -292,7 +292,7 @@ void FixStorePeratom::unpack_restart(int nlocal, int nth)
maxsize of any atom's restart data
------------------------------------------------------------------------- */
int FixStorePeratom::maxsize_restart()
int FixStoreAtom::maxsize_restart()
{
if (disable) return 1;
return nvalues + 1;
@ -302,17 +302,17 @@ int FixStorePeratom::maxsize_restart()
size of atom nlocal's restart data
------------------------------------------------------------------------- */
int FixStorePeratom::size_restart(int /*nlocal*/)
int FixStoreAtom::size_restart(int /*nlocal*/)
{
if (disable) return 1;
return nvalues + 1;
}
/* ----------------------------------------------------------------------
memory usage of global or peratom atom-based array
memory usage of per-atom atom-based array
------------------------------------------------------------------------- */
double FixStorePeratom::memory_usage()
double FixStoreAtom::memory_usage()
{
return (double) atom->nmax * nvalues * sizeof(double);
}

12
src/fix_store_peratom.h → src/fix_store_atom.h
View File

@ -13,26 +13,26 @@
#ifdef FIX_CLASS
// clang-format off
FixStyle(STORE/PERATOM,FixStorePeratom);
FixStyle(STORE/ATOM,FixStoreAtom);
// clang-format on
#else
#ifndef LMP_FIX_STORE_PERATOM_H
#define LMP_FIX_STORE_PERATOM_H
#ifndef LMP_FIX_STORE_ATOM_H
#define LMP_FIX_STORE_ATOM_H
#include "fix.h"
namespace LAMMPS_NS {
class FixStorePeratom : public Fix {
class FixStoreAtom : public Fix {
public:
double *vstore; // vector storage
double **astore; // array storage
double ***tstore; // tensor (3d array) storage
int disable; // 1 if operations (except grow) are currently disabled
FixStorePeratom(class LAMMPS *, int, char **);
~FixStorePeratom() override;
FixStoreAtom(class LAMMPS *, int, char **);
~FixStoreAtom() override;
int setmask() override;
void grow_arrays(int) override;

2
src/fix_store_global.cpp
View File

@ -182,7 +182,7 @@ void FixStoreGlobal::restart(char *buf)
}
/* ----------------------------------------------------------------------
memory usage of global or peratom atom-based array
memory usage of global data
------------------------------------------------------------------------- */
double FixStoreGlobal::memory_usage()

6
src/variable.cpp
View File

@ -20,7 +20,7 @@
#include "domain.h"
#include "error.h"
#include "fix.h"
#include "fix_store_peratom.h"
#include "fix_store_atom.h"
#include "group.h"
#include "info.h"
#include "input.h"
@ -5027,8 +5027,8 @@ VarReader::VarReader(LAMMPS *lmp, char *name, char *file, int flag) :
error->all(FLERR,"Cannot use atomfile-style variable unless an atom map exists");
id_fix = utils::strdup(std::string(name) + "_VARIABLE_STORE");
fixstore = dynamic_cast<FixStorePeratom *>(
modify->add_fix(std::string(id_fix) + " all STORE/PERATOM 1 0 0 0"));
fixstore = dynamic_cast<FixStoreAtom *>(
modify->add_fix(std::string(id_fix) + " all STORE/ATOM 1 0 0 0"));
buffer = new char[CHUNK*MAXLINE];
}
}

2
src/variable.h
View File

@ -152,7 +152,7 @@ class Variable : protected Pointers {
class VarReader : protected Pointers {
public:
class FixStorePeratom *fixstore;
class FixStoreAtom *fixstore;
char *id_fix;
VarReader(class LAMMPS *, char *, char *, int);